The AVR109 butterfly protocol does not support access to the user signature row and the production signature row on XMega devices. The XBoot bootloader adds support for these locations by adding the memory types "U" and "P" in addition to the existing "E" and "F" types.

Updating AVRDUDE to support this would be trivial - it involves adding a couple of additional conditions to the block read and write fuctions in butterfly.c. The only question is whether or not to add them universally and check for error conditions or to only support them for specific bootloaders.